TRACY BOWDEN, PRESENTER: Japan's season of whaling in the Southern Ocean is now in full swing but the game is rapidly changing.

Three Australian activists who boarded a Japanese whaling support ship on the weekend are in the custody of the crew and reportedly threatening a hunger strike, with no official word yet on when they'll be released.

And the Japanese government now says it's lodged a formal protest.

Were the activists within their rights?

Mary Gearin reports.

CAPTAIN PAUL WATSON, SEA SHEPHERD: We have no communication with them. They're being held prisoner and incommunicado.

(Footage courtesy of Sea Shepherd of a boat at night, people climbing up the side, saying, "Go, go, go, go.")

PAUL WATSON: Australia could get them off that boat if they wanted to. They know that. But they you know, they're going to just sacrifice them in the interests of appeasing Japan.

NICOLA ROXON, FEDERAL ATTORNEY-GENERAL: The normal laws of the sea mean that the flag of the ship that's at question is normally how you determine what law applies. And in this case obviously that's Japan.

MARY GEARIN: Just days after Sea Shepherd activists attacked the whaling boat Yushin Maru 3, under the cover of night three Forest Rescue members boarded the whaling support vessel Shonan Maru 2 and sank two governments into a legal and diplomatic challenge.

PAUL WATSON: I think they're brave and I think what they did was motivated out of frustration at the lack of action by the Australian Government which promised to do something and has never done anything.

ASSOCIATE PROFESSOR TIM STEPHENS, UNIVERSITY OF SYDNEY: What we are seeing from these environmental groups is a tremendously well calculated or carefully calculated stunt to raise a number of different legal and political issues in order to achieve an objective.

But really it doesn't change any of the underlying questions about the lawfulness or otherwise of what Japan is currently doing in the Southern Ocean.

MARY GEARIN: The first issue in dispute is about exactly where this happened.

The Federal Attorney-General says it took place in Australia's exclusive economic zone where the nation's rights are limited.

NICOLA ROXON: The clear area where Australia has a right to exert its laws and authority is within our territorial waters. No-one is claiming that this occurred within our territorial waters.

The exclusive economic zone is really focussed on what rights as a coastal state we are able to exercise in exploiting whether it's oil or fish or other sorts of resources. It doesn't mean that our laws apply.

MARY GEARIN: A spokesman for the Institute for Cetacean Research that conducts the whaling missions on behalf of the Japanese government backs up this version.

GLENN INWOOD, SPOKESMAN ICR: The Japanese government has clarified where the incident occurred. And it was 40 kilometres off the coast of Bunbury. So it was outside of Australia's territorial waters over which it has full sovereignty.

MARY GEARIN: But the Sea Shepherd organisation says it had two boats at the site of the boarding and claims it happened in the so-called contiguous zone, closer to shore.

PAUL WATSON: It was just very unethical for Attorney-General just to take the word of the whalers on this.

The Australian Government really should do their homework before making statements like that. It was 16 miles off the coast, inside the contiguous zone. And that's easily proven because the vessels have GPS units which record their position at the time.

According to the regulations that Australian Customs and Immigration have absolute authority in that contiguous zone.

These are three Australian citizens taken out of Aust territory without a passport and without clearance from the Australian authorities.

GLENN INWOOD: They haven't been taken. Those men voluntarily got on board that vessel and then the inflatable sped away.

It's entirely up to Japan on what to do with them.

TIM STEPHENS: Legally there's very little we can do Mary. The Japanese have a complete entitlement to hold these men.

MARY GEARIN: Associate professor Tim Stephens is the director for the Sydney Centre for International Law at Sydney University.

He says even if the incident happened in the contiguous zone it would be impossible to argue that the activists couldn't be taken away by the Japanese vessel because the trio boarded it voluntarily.

TIM STEPHENS: So far as Japan is concerned it can hold these three protesters and can take them back to Japan if it wishes to.

NICOLA ROXON: We are very concerned to make sure that they are in a healthy condition. We've asked for direct consular access. That hasn't yet been granted but we will continue to pursue that.

GLENN INWOOD: Presently the Shonan Maru number 2 is trailing the Steve Irwin and the three men remain on board. They are being well cared for, fed if they want it and being kept (inaudible) watch.

But at this stage they will have to remain on that vessel until such time as the government of Japan makes a decision on what to do.

This is unchartered waters for everyone.

The capture of New Zealand activist Peter Bethune in 2010 after he boarded the same boat to make a citizen's arrest on its captain was in an international zone.

He was held in Japan for five months before being given a two year suspended sentence.

TIM STEPHENS: What is absolutely fascinating is how the environmental groups are seeking to up the ante as it were.

And so just a real matter of winding up the pressure and the tension and creating all kinds of headaches for the governments concerned.

MARY GEARIN: In fact anti-whaling protests have entered a new phase.

(Sound of whale song recordings being played from a vehicle at protest)

The new activists to hop on board are from Forest Rescue Australia.

MICHAEL MONTGOMERY, FOREST RESCUE AUSTRALIA: The motivation was definitely to bring attention to what's happening. The motivation was also to get them off the Sea Shepherd's tail.

MARY GEARIN: The question is, will more activists join such action and will it actually stop whaling?

JULIE MACKEN, SPOKESWOMAN, GREENPEACE: What we would really like to see is for people and for us as Australians to have a national conversation about how do we protest, how do we do this in a principled way that achieves our outcomes without imperilling anyone's lives in the process.

MARY GEARIN: Greenpeace abandoned nautical engagement some time ago.

JULIE MACKEN: We believe having done that for the last two decades, for us the fight is to be had and is to be won in Japan, working with civil society, and the Japan people to collapse this obscene trade in whale meat.

PAUL WATSON: Our tactics are the only tactics that have saved whales. Nobody else saved a single whale down there except for Sea Shepherd's intervention.

Australia's position going to the international court is one that will take years and even if it's resolved Japan will simply ignore the results and do what it's doing.

MARY GEARIN: What Greenpeace, Sea Shepherd, the opposition and the Greens all have in common is their call for the Government to send observers.

But the Government instead is relying on action in the International Court of Justice that may take one or two more whaling seasons to be resolved.